Merge pull request #232 from mrc-ide/mrc-5976

Mrc 5976 - use github actions and ghcr

.github/actions/build-and-run-wodin/action.yml

@@ -0,0 +1,15 @@
+name: Build and run WODIN (and deps)
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-node@v4
+      with:
+        node-version: 20
+
+    - name: Build and run server
+      shell: bash
+      run: |
+        ./scripts/build.sh
+        ./scripts/run-dependencies.sh
+        npm run serve --prefix=app/server &

.github/actions/ci-env-and-ghcr-login/action.yml

@@ -0,0 +1,39 @@
+name: Setup CI Env and login to GHCR
+
+inputs:
+  ghcr-username:
+    required: true
+  ghcr-password:
+    required: true
+
+outputs:
+  CI_SHA:
+    description: "Short SHA of current commit"
+    value: ${{ steps.ci-env.outputs.CI_SHA }}
+  CI_BRANCH:
+    description: "Current branch"
+    value: ${{ steps.ci-env.outputs.CI_BRANCH }}
+
+runs:
+  using: "composite"
+  steps:
+    - id: ci-env
+      name: Setup Environment
+      shell: bash
+      run: |
+        if [ "${{github.event_name}}" = "pull_request" ];
+        then
+          long_sha=${{ github.event.pull_request.head.sha }}
+          echo "CI_BRANCH=${{ github.head_ref }}" >> $GITHUB_OUTPUT
+        else
+          long_sha=${GITHUB_SHA}
+          echo "CI_BRANCH=${{ github.ref_name }}" >> $GITHUB_OUTPUT
+        fi
+        echo "CI_SHA=${long_sha:0:7}" >> $GITHUB_OUTPUT
+
+    - name: Login to GHCR (GitHub Packages)
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ inputs.ghcr-username }}
+        password: ${{ inputs.ghcr-password }}

.github/actions/install-npm-packages/action.yml

@@ -0,0 +1,28 @@
+name: Install NPM packages
+
+inputs:
+  server:
+    required: false
+    default: 'false'
+  static:
+    required: false
+    default: 'false'
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-node@v4
+      with:
+        node-version: 20
+
+    - name: Install server (backend) NPM packages
+      if: inputs.server == 'true'
+      shell: bash
+      run: |
+        npm ci --prefix=app/server
+
+    - name: Install static (frontend) NPM packages
+      if: inputs.static == 'true'
+      shell: bash
+      run: |
+        npm ci --prefix=app/static

.github/workflows/build-test-publish.yml

@@ -0,0 +1,135 @@
+name: CI
+
+on: [push]
+
+env:
+  TAG_GHCR: mrc-ide/wodin
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - id: ci-env
+        uses: ./.github/actions/ci-env-and-ghcr-login
+        with:
+          ghcr-username: ${{ github.actor }}
+          ghcr-password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push docker
+        uses: docker/build-push-action@v5
+        with:
+          file: ./docker/Dockerfile
+          push: true
+          tags: |
+            ghcr.io/${{ env.TAG_GHCR }}:${{ steps.ci-env.outputs.CI_SHA }}
+            ghcr.io/${{ env.TAG_GHCR }}:${{ steps.ci-env.outputs.CI_BRANCH }}
+      - name: Smoke test
+        run: |
+          ./scripts/run-version.sh --app ${{ steps.ci-env.outputs.CI_BRANCH }} &
+          ./scripts/smoke-test.sh
+
+  fe-unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/install-npm-packages
+        with:
+          static: true
+
+      - name: Test front end
+        run: npm run coverage --prefix=app/static
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          files: ./app/static/coverage/coverage-final.json
+          token: ${{ secrets.CODECOV_TOKEN }}
+          codecov_yml_path: ./codecov.yml
+
+  be-unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-and-run-wodin
+
+      - name: Test back end
+        run: npm test --prefix=app/server
+      - name: Check versions
+        run: npm run genversion --prefix=app/server -- --check-only
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true # optional (default = false)
+          files: ./app/server/coverage/coverage-final.json
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+
+  integration-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-and-run-wodin
+
+      - name: Test back end integration
+        run: npm run integration-test --prefix=app/server
+
+  playwright-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        shard: [1, 2, 3, 4, 5, 6]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-and-run-wodin
+
+      - name: Get installed Playwright version
+        run: echo "PLAYWRIGHT_VERSION=$(node -e "console.log(require('./app/static/package-lock.json').packages['node_modules/@playwright/test'].version)")" >> $GITHUB_ENV
+      - name: Cache binaries for playwright version
+        uses: actions/cache@v4
+        id: playwright-cache
+        with:
+          path: |
+            ~/.cache/ms-playwright
+          key: ${{ runner.os }}-playwright-${{ env.PLAYWRIGHT_VERSION }}
+      - name: Install Playwright Browsers
+        if: steps.playwright-cache.outputs.cache-hit != 'true'
+        run: npx playwright@${{ env.PLAYWRIGHT_VERSION }} install --with-deps
+      - name: Test e2e
+        run: npm run test:e2e --prefix=app/static -- --shard=${{ matrix.shard }}/6
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/install-npm-packages
+        with:
+          static: true
+          server: true
+
+      - name: Lint back end
+        run: npm run lint --prefix=app/server
+      - name: Lint front end
+        run: npm run lint --prefix=app/static
+
+  publish-latest-image:
+    runs-on: ubuntu-latest
+    # change this ref to publish to "latest" tag from another branch
+    if: github.ref == 'refs/heads/main'
+    needs: [build-and-push, fe-unit-tests, be-unit-tests, integration-tests, playwright-tests, lint]
+    steps:
+      - uses: actions/checkout@v4
+      - id: ci-env
+        uses: ./.github/actions/ci-env-and-ghcr-login
+        with:
+          ghcr-username: ${{ github.actor }}
+          ghcr-password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish image manifest to latest
+        run: |
+          GHCR_TOKEN=$(echo ${{ secrets.GITHUB_TOKEN }} | base64)
+          curl "https://ghcr.io/v2/mrc-ide/wodin/manifests/${{ steps.ci-env.outputs.CI_BRANCH }}" \
+          -H "accept: application/vnd.docker.distribution.manifest.v2+json" \
+          -H "Authorization: Bearer ${GHCR_TOKEN}" \
+          > manifest.json
+          curl -XPUT "https://ghcr.io/v2/mrc-ide/wodin/manifests/latest" \
+          -H "content-type: application/vnd.docker.distribution.manifest.v2+json" \
+          -H "Authorization: Bearer ${GHCR_TOKEN}" \
+          -d '@manifest.json'

app/static/playwright.config.ts

@@ -26,8 +26,7 @@ export default defineConfig({
   forbidOnly: !!process.env.CI,
   /* Retry on CI only */
   retries: process.env.CI ? 2 : 1,
-  /* Opt out of parallel tests on CI. */
-  workers: process.env.CI ? 1 : undefined,
+  fullyParallel: true,
   /* Reporter to use. See https://playwright.dev/docs/test-reporters */
   // reporter: 'html',
   /* Shared settings for all the projects below. See https://playwright.dev/docs/api/class-testoptions. */
@@ -54,16 +53,4 @@ export default defineConfig({
 
   /* Folder for test artifacts such as screenshots, videos, traces, etc. */
   // outputDir: 'test-results/',
-
-  /* Run your local dev server before starting the tests */
-  webServer: {
-    /**
-     * Use the dev server by default for faster feedback loop.
-     * Use the preview server on CI for more realistic testing.
-     * Playwright will re-use the local server if there is already a dev-server running.
-     */
-    command: process.env.CI ? 'npm run build' : 'npm run dev',
-    port: 5173,
-    reuseExistingServer: !process.env.CI
-  }
 })

app/static/tests/e2e/index.etest.ts

@@ -3,17 +3,18 @@ import * as fs from "fs";
 import { realisticFitData } from "./utils";
 
 test.describe("Index tests", () => {
-    const tmpPath = "tmp";
+    let tmpPath: string;
 
-    test.beforeAll(() => {
+    test.beforeEach(() => {
+        tmpPath = `${Math.random()}`;
         if (fs.existsSync(tmpPath)) {
-            fs.rmdirSync(tmpPath, { recursive: true });
+            fs.rmSync(tmpPath, { recursive: true });
         }
         fs.mkdirSync(tmpPath);
     });
 
-    test.afterAll(() => {
-        fs.rmdirSync(tmpPath, { recursive: true });
+    test.afterEach(() => {
+        fs.rmSync(tmpPath, { recursive: true });
     });
 
     test("renders heading", async ({ page }) => {

app/static/tests/e2e/stochastic.etest.ts

@@ -1,16 +1,21 @@
-import { expect, test } from "@playwright/test";
-import PlaywrightConfig from "../../playwright.config";
+import { expect, Page, test } from "@playwright/test";
 import { expectSummaryValues } from "./utils";
 
 test.describe("stochastic app", () => {
-    const { timeout } = PlaywrightConfig;
-
     test.beforeEach(async ({ page }) => {
         await page.goto("/apps/day3");
         await page.click(":nth-match(.wodin-left .nav-tabs a, 2)"); // Options
         await page.click(":nth-match(.wodin-right .nav-tabs a, 2)"); // Run
     });
 
+    const expectChangedNumberOfReplicatesMessage = async (page: Page, newReplicates: string) => {
+        await expect(await page.locator(".action-required-msg")).toHaveText("");
+        await page.fill(":nth-match(#run-options input, 2)", newReplicates);
+        await expect(await page.locator(".action-required-msg")).toHaveText(
+            "Plot is out of date: number of replicates has changed. Run model to update."
+        );
+    };
+
     test("can display number of replicates", async ({ page }) => {
         await expect(await page.innerText(":nth-match(.collapse-title, 2)")).toContain("Run Options");
         await expect(await page.getAttribute(":nth-match(.collapse-title i, 2)", "data-name")).toBe("chevron-up");
@@ -22,18 +27,11 @@ test.describe("stochastic app", () => {
     });
 
     test("can change number of replicates and re-run model", async ({ page }) => {
-        await page.fill(":nth-match(#run-options input, 2)", "6");
-
-        await expect(await page.locator(".run-tab .action-required-msg")).toHaveText(
-            "Plot is out of date: number of replicates has changed. Run model to update.",
-            {
-                timeout
-            }
-        );
+        await expectChangedNumberOfReplicatesMessage(page, "6");
 
         // Re-run model
         await page.click("#run-btn");
-        await expect(await page.locator(".run-tab .action-required-msg")).toHaveText("");
+        await expect(await page.locator(".action-required-msg")).toHaveText("");
 
         // number of series should have increased by 2
         const summary = ".wodin-plot-data-summary-series";
@@ -48,30 +46,18 @@ test.describe("stochastic app", () => {
     });
 
     test("traces are hidden if replicates are above maxReplicatesDisplay", async ({ page }) => {
-        await page.fill(":nth-match(#run-options input, 2)", "50");
-        await expect(await page.locator(".run-tab .action-required-msg")).toHaveText(
-            "Plot is out of date: number of replicates has changed. Run model to update.",
-            {
-                timeout
-            }
-        );
+        await expectChangedNumberOfReplicatesMessage(page, "50");
 
         await page.click("#run-btn");
-        await expect(await page.locator(".run-tab .action-required-msg")).toHaveText("");
+        await expect(await page.locator(".action-required-msg")).toHaveText("");
 
         const summary = ".wodin-plot-data-summary-series";
         expect(await page.locator(summary).count()).toBe(104);
 
-        await page.fill(":nth-match(#run-options input, 2)", "51");
-        await expect(await page.locator(".run-tab .action-required-msg")).toHaveText(
-            "Plot is out of date: number of replicates has changed. Run model to update.",
-            {
-                timeout
-            }
-        );
+        await expectChangedNumberOfReplicatesMessage(page, "51");
 
         await page.click("#run-btn");
-        await expect(await page.locator(".run-tab .action-required-msg")).toHaveText("");
+        await expect(await page.locator(".action-required-msg")).toHaveText("");
 
         expect(await page.locator(summary).count()).toBe(4);
 
@@ -93,7 +79,7 @@ test.describe("stochastic app", () => {
 
         // Can see summary traces
         const summary = ".wodin-plot-data-summary-series";
-        await expect(await page.locator(summary)).toHaveCount(44, { timeout });
+        await expect(await page.locator(summary)).toHaveCount(44);
 
         await expectSummaryValues(page, 1, "I_det (beta=0.450)", 1001, "#2e5cb8");
         await expectSummaryValues(page, 2, "I (beta=0.450)", 1001, "#6ab74d");